Re: [gmx-users] unit conversions
Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Ramachandran G wrote: Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. If you are not comparing the same force fields, you are not likely to get the same answer. I thought I identified the fact that the value you are referring to corresponds to the MOIL implementation of OPLS-UA, which has no relationship whatsoever to the Gromacs implementation of CHARMM. Dividing by 4.184 is the correct conversion factor for kcal-kJ. -Justin with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
Re: [gmx-users] unit conversions
Thank you for your clarification. Rama On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. If you are not comparing the same force fields, you are not likely to get the same answer. I thought I identified the fact that the value you are referring to corresponds to the MOIL implementation of OPLS-UA, which has no relationship whatsoever to the Gromacs implementation of CHARMM. Dividing by 4.184 is the correct conversion factor for kcal-kJ. -Justin with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada,
